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Saccharomyces cerevisiae
9 Downloadable Samples
Illumina HiSeq 2000
Description
The cysteine-rich PLAC8 domain occurs in proteins found in the majority of Eukaryotes. PLAC8-containing proteins play important yet diverse roles in different organisms, such as control of cell proliferation in animals and plants or heavy metals resistance in plants and fungi. For example, Onzin from Mus musculus is a key regulator of cell proliferation, whereas FCR1 from the ascomycete Oidiodendron maius is involved in cadmium resistance. We compared these two PLAC8-containing proteins by heterologous expression in the PLAC8-free yeast Saccharomyces cerevisiae in order to identify possible common functions. When expressed in yeast, both Onzin and FCR1 improved yeast cadmium resistance, reduced cadmium-induced DNA mutagenesis, localized in the nucleus and induced similar transcriptional changes. Our results support the hypothesis of a common ancestral function of the PLAC8 domain that may link Fe-S cluster biogenesis, iron homeostasis and the control of DNA damage, thus opening new perspectives to understand the role of this protein domain in the cellular biology of eukaryotes.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
View Samples- Homo sapiens
- 96 Downloadable Samples
- IlluminaHiSeq1000
Description
K562 single cell RNA-seq study
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples
SRP183700- Homo sapiens
- 30 Downloadable Samples
- NextSeq 500
Description
We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA).
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- NextSeq 500
Description
Estrogens have been shown to elicit anti-cancer effects against estrogen receptor alpha (ER)-positive breast cancer. We sought to determine the underlying mechanism of therapeutic response. Response to estrogen treatment was assessed in ER+ breast cancer models of anti-estrogen resistant disease: WHIM16 patient-derived xenografts, C7-2-HI and C4-HI murine mammary adenocarcinomas, and long-term estrogen-deprived MCF-7 cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- NextSeq 500
Description
Microenvironmental secreted factor screening revealed cytokines that modulate drug sensitivity in ER+ breast cancer cells. BMP4 was a top hit that is not normally expressed in ER+ breast cancer, and was found to enhance efficacy of anti-estrogens and CDK4/6i in anti-estrogen-sensitive and -resistant ER+ breast cancer cells. The anti-cancer effects of BMP4 were mediated by ALK3 and canonical BMP pathway signaling, leading to downstream p21 induction and cell cycle arrest. The clinical relevance of this phenotype was confirmed in analyses of 3 cohorts of patients with ER+ breast cancer, highlighting BMP4 pathway activation as a potential therapeutic opportunity in ER+ breast cancer.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Arabidopsis thaliana
- 14 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The transcriptional response of Arabidopsis thaliana cell suspensions following treatment with the stress hormone methyl jasmonate (MeJA) was monitored over time 16 hours after subcultivation. Three time points were included: 30 minutes, 2 hours and 6 hours after elicitation with 50µm MeJA or DMSO as a control.
Publication Title
Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells.
Sample Metadata Fields
Compound, Time
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Global restriction of protein synthesis is a hallmark of cellular stress. Using hydrogen peroxide, we monitor the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analysed.
Publication Title
Global translational responses to oxidative stress impact upon multiple levels of protein synthesis.
Sample Metadata Fields
Sex, Compound
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
One common form of translational control is mediated by proteins that bind to the mRNA 5' cap-binding protein eIF4E. These proteins are collectively called 4E binding proteins (4EBPs). Saccharomyces cerevisiae possesses two 4EBPs that are encoded by non-essential genes called CAF20 and EAP1. To determine the impact of gene deletion on gene expression, we monitored the transcript level and also the translation status for each RNA using cycloheximide to freeze elongating ribosomes in wild-type, caf20 and eap1 cells. Polyribosome fractionation of cell extracts was used to separate highly translated and poorly translated mRNAs that were then separately analyzed.
Publication Title
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Compare m1A levels in the 16S (large) mitochondrial ribosomal RNA in TRMT61B knockdown cells and control.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina Genome Analyzer II
Description
The data contains RNA sequencing data of embryonic stem cell derived cells.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples